ProInflam: a webserver for the prediction of proinflammatory antigenicity of peptides and proteins

Additional file 2: Table S2. Dipeptide composition distribution between proinflammatory and non proinflammatory data

(TG/CA)(n )repeats in human gene families: abundance and selective patterns of distribution according to function and gene length

BACKGROUND: Creation of human gene families was facilitated significantly by gene duplication and diversification. The (TG/CA)(n )repeats exhibit length variability, display genome-wide distribution, and are abundant in the human genome. Accumulation of evidences for their multiple functional roles including regulation of transcription and stimulation of recombination and splicing elect them as functional elements. Here, we report analysis of the distribution of (TG/CA)(n )repeats in human gene families. RESULTS: The 1,317 human gene families were classified into six functional classes. Distribution of (TG/CA)(n )repeats were analyzed both from a global perspective and from a stratified perspective based on their biological properties. The number of genes with repeats decreased with increasing repeat length and several genes (53%) had repeats of multiple types in various combinations. Repeats were positively associated with the class of Signaling and communication whereas, they were negatively associated with the classes of Immune and related functions and of Information. The proportion of genes with (TG/CA)(n )repeats in each class was proportional to the corresponding average gene length. The repeat distribution pattern in large gene families generally mirrored the global distribution pattern but differed particularly for Collagen gene family, which was rich in repeats. The position and flanking sequences of the repeats of Collagen genes showed high conservation in the Chimpanzee genome. However the majority of these repeats displayed length polymorphism. CONCLUSION: Positive association of repeats with genes of Signaling and communication points to their role in modulation of transcription. Negative association of repeats in genes of Information relates to the smaller gene length, higher expression and fundamental role in cellular physiology. In genes of Immune and related functions negative association of repeats perhaps relates to the smaller gene length and the directional nature of the recombinogenic processes to generate immune diversity. Thus, multiple factors including gene length, function and directionality of recombinogenic processes steered the observed distribution of (TG/CA)(n )repeats. Furthermore, the distribution of repeat patterns is consistent with the current model that long repeats tend to contract more than expand whereas, the reverse dynamics operates in short repeats

Prediction of peptidoglycan hydrolases- a new class of antibacterial proteins

Comparison of performance of the three approaches using known 250 peptidoglycan hydrolases. (XLSX 8 kb

ArrayD: A general purpose software for Microarray design

BACKGROUND: Microarray is a high-throughput technology to study expression of thousands of genes in parallel. A critical aspect of microarray production is the design aimed at space optimization while maximizing the number of gene probes and their replicates to be spotted. RESULTS: We have developed a software called 'ArrayD' that offers various alternative design solutions for an array given a set of user requirements. The user feeds the following inputs: type of source plates to be used, number of gene probes to be printed, number of replicates and number of pins to be used for printing. The solutions are stored in a text file. The choice of a design solution to be used will be governed by the spotting chemistry to be used and the accuracy of the robot. CONCLUSIONS: ArrayD is a software for standard cartesian robots. The software aids users in preparing a judicious and elegant design. ArrayD is universally applicable and is available at

Assessing natural variations in gene expression in humans by comparing with monozygotic twins using microarrays

Quantitative variation in gene expression in humans is the outcome of various factors, including differences in genetic background, gender, age, and environment. However, the extent of the influence of these factors on gene expression is not clear. We attempted to address this issue by carrying out gene expression profiling in blood leukocytes with 13 individuals (including 5 pairs of monozygotic twins) on 10,000 genes using HG-U95Av2 oligonucleotide microarrays. The proportion of differentially expressed genes between monozygotic twins was low (up to 1.76%). Most of the variations belonged to the least variable category. These genes, exhibiting "random variations," did not show clear preference to any functional class, although "signaling and communication" and "immune and related functions" generally topped the list. The extent of variation in gene expression increased in comparisons between unrelated individuals (up to 14.13%). Most of the genes (89%) exhibiting random variations in twins also varied in expression in unrelated individuals. As with twins, signaling and communication topped the list, and substantial variations were observed in all three categories: least variable, moderately variable, and most variable. An important outcome of this study was that the housekeeping genes were nearly insensitive to random variations but appeared to be more susceptible to genetic differences. However, the highly expressed housekeeping genes exhibited low variation and appeared to be insensitive to all known factors. Gene expression profiling in monozygotic twins can provide useful data for the assessment of natural variation in gene expression in humans

Complete Genome Sequences of Arcobacter butzleri ED-1 and Arcobacter sp Strain L, Both Isolated from a Microbial Fuel Cell

Arcobacter butzleri strain ED-1 is an exoelectrogenic epsilonproteobacterium isolated from the anode biofilm of a microbial fuel cell. Arcobacter sp. strain L dominates the liquid phase of the same fuel cell. Here we report the finished and annotated genome sequences of these organisms

CIFKAS A Measurer of Functional Disability Status in Knee Osteoarthritis

Knee osteoarthritis (OA) results in structural and functional abnormalities and reduced functional performance abilities. In developing countries majority of population lives in rural areas having limited resources and socio-cultural biodiversity. Their personal, socio-cultural and occupational habits vary and need to be addressed. So a culturally relevant and contextually appropriate, Composite Indian Functional Knee Assessment Scale (CIFKAS) for measuring the functional status in knee osteoarthritis was formulated. 128 participants from various geographical regions of India of age range 40 to 60 years using convenient sampling were included and informed consent signed by the participants. Each participant was assigned to one of the two groups. 39 participants in group A reported no episode of knee pain while 89 participants in group B reported at least one episode of knee pain in the last two months. Each participant was assessed on Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) and CIFKAS and statistical analysis was done. The Pearson correlation coefficient calculated for all 128 subjects for pain, physical functional abilities and total functional disability score were 0.878, 0.925 and 0.945 respectively. Between group analysis was done using Independent t test and p value was found to be not significant for pain (≤178), highly significant for physical functional abilities (p≤0001) and very significant for total functional disability status score (p≤004). The results indicate that both WOMAC and CIFKAS are highly correlated and there is no difference between the two for measuring pain, but for functional ability and overall functional disability status within their functional context, CIFKAS is a better tool than WOMAC.KEYWORDS: Knee osteoarthritis; Functional disability; Socio-cultural biodiversities; Functional contextInternet Journal of Medical Update 2012 January;7(1):47-5

Melting of Quarkonia in strong magnetic field

In this paper, spectra of the quarkonium states has been studied using the conditions temperature, chemical potential and the magnetic field. Here our main focus is to study the effect of strong magnetic field on the quarkonium properties. The binding energies and the dissociation temperature for the ground and the first excited states of the charmonium and bottomonium in the presence of strong magnetic field at chemical potential μ = 500 MeV has been studied. Here we use quasiparticle(QP) Debye mass depending upon temperature, magnetic field and chemical potential obtained from the quasiparticle approach. The Debye mass strongly increases at different values of temperature and magnetic field. The binding energy decreases with increase in the temperature at different magnetic field eB=0.3, 0.5, and 0.7 GeV2 and also decreases with magnetic field at different at T=200,300 and 400 MeV for the J/ψ, Ψ’, ϒ, and ϒ’ states of the quarkonia. The dissociation temperature of the quarkonium states falls with the increasing values of the magnetic field at critical temperature Tc =197 MeV

Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats

BACKGROUND: Quantitative variation in gene expression has been proposed to underlie phenotypic variation among human individuals. A facilitating step towards understanding the basis for gene expression variability is associating genome wide transcription patterns with potential cis modifiers of gene expression. DESCRIPTION: EXPOLDB, a novel Database, is a new effort addressing this need by providing information on gene expression levels variability across individuals, as well as the presence and features of potentially polymorphic (TG/CA)(n )repeats. EXPOLDB thus enables associating transcription levels with the presence and length of (TG/CA)(n )repeats. One of the unique features of this database is the display of expression data for 5 pairs of monozygotic twins, which allows identification of genes whose variability in expression, are influenced by non-genetic factors including environment. In addition to queries by gene name, EXPOLDB allows for queries by a pathway name. Users can also upload their list of HGNC (HUGO (The Human Genome Organisation) Gene Nomenclature Committee) symbols for interrogating expression patterns. The online application 'SimRep' can be used to find simple repeats in a given nucleotide sequence. To help illustrate primary applications, case examples of Housekeeping genes and the RUNX gene family, as well as one example of glycolytic pathway genes are provided. CONCLUSION: The uniqueness of EXPOLDB is in facilitating the association of genome wide transcription variations with the presence and type of polymorphic repeats while offering the feature for identifying genes whose expression variability are influenced by non genetic factors including environment. In addition, the database allows comprehensive querying including functional information on biochemical pathways of the human genes. EXPOLDB can be accessed a

Cultural studies on Ustilaginoidea virens, the incitant of false smut of rice (Oryza sativa)

A study was carried out to find out the favourable culture media for mass multiplication and the effect of carbon sources and duration on chlamydospore germination of Ustilaginoidea virens (Cook.) Tak. Different synthetic and semi synthetic solid, liquid media, substrate media were evaluated for mass multiplication of U. virens. Potato sucrose broth was the best medium for fast mycelia growth (104.80 mg) and sporulation (6.78 × 105 spores/ml), potato dextrose broth also favored mycelial growth, whereas corn meal dextrose broth was not suitable. Out of four solid media tested, maximum colony diameter (68.74 mm) and sporulation (6.86 × 105 spores/ml) was produced by potato sucrose agar followed by potato dextrose agar. Maximum sporulation was produced on substrate media based on barley seeds (5.54 × 105 spores/ml) followed by rice seeds (3.72 × 105 spores/ml) whereas rice husk based media produced minimum sporulation. Higher concentration of sucrose and dextrose at 2 per cent supported maximum germination of spores of U. virens and sucrose was found superior in inducing germination than dextrose. The results of this study help to understand the physiological and biochemical requirements for the growth and development of the pathogen, which could serve as an input in disease management to minimize the effect of false smut disease on rice